version: 30 August, 2024

GitHub repository

About this document

All analyses preformed with R version 4.2.2.

Basic setup of R environment

Loading required packages

For the following analyses we will require the use of a number of different R packages. We can use the following code to quickly load in the packages and install any packages not previously installed in the R console.

if (!require("pacman")) install.packages("pacman")

pacman::p_load_gh("pmartinezarbizu/pairwiseAdonis/pairwiseAdonis", "ropensci/rnaturalearthhires", "KarstensLab/microshades")

pacman::p_load("cowplot", "car", "ggrepel", "ggspatial", "ggstance", "ggtreeExtra", "ggtree", "paletteer", "patchwork", "rgdal", "rnaturalearth", "sf", "Hmisc", "MCMC.OTU", "pairwiseAdonis", "RColorBrewer", "Redmonder", "flextable", "lubridate", "officer", "adegenet", "dendextend", "gdata", "ggdendro", "hierfstat", "kableExtra", "poppr", "reshape2", "StAMPP", "vcfR", "vegan", "boa", "magick", "rgeos", "sdmpredictors", "ggcorrplot", "tidyverse", "TeachingDemos", "LaplacesDemon", "adespatial", "ggnewscale", "ggbeeswarm", "multcomp", "rstatix", "R.utils", "graph4lg")

options("scipen" = 10)

# load("fknmsSint.RData")

Themes and colors

Making color palettes to use throughout all plots

# flPal = c("#401718",  "#802d2f",  "#ff595e",  "#ff924c",  "#f8e16f", "#95cf92",  "#369acc",  "#9656a2",  "#cbabd1")[c(2:9)]
# flPal = c("#401718",  "#802d2f",  "#ff595e",  "#FF914D",  "#f8e16f", "#95cf92",  "#369acc",  "#9656a2",  "#cbabd1")[c(2:9)]

flPal = paletteer_c(`"viridis::turbo"`, 9, direction = -1)[c(2:9)]

# paletteer_d("vapoRwave::vapoRwave")[10])

pink = "#FF6A8BFF"
purple = paletteer_d("vapoRwave::vapoRwave")[10]

# xestoKColPal = c( "#A21150", "#D84D7A", "#E57D7E", "#EBA396", "#F2C5B1")

xestoKColPal = c( "#800E52", "#FF2879", "#E66060", "#FF866B", "#FF8F8F", "#BB3571")
#"#F32BA3"

Plot themes

dendTheme = theme(axis.title.x = element_blank(),
  axis.text.x = element_blank(),
  axis.line.x = element_blank(),
  axis.ticks.x = element_blank(),
  axis.title.y = element_text(size = 10, color = "black", angle = 90),
  axis.text.y = element_text(size = 8, color = "black"),
  axis.line.y = element_line(),
  axis.ticks.y = element_line(),
  panel.grid = element_blank(),
  panel.border = element_blank(),
  panel.background = element_blank(),
  legend.key.size = unit(0.75, "line"),
  legend.key = element_blank(),
  legend.title = element_text(size = 10),
  legend.text = element_text(size = 8),
  legend.direction = "horizontal",
  legend.box = "vertical",
  legend.position = c(0.13, 0.1))

pcaTheme = theme(axis.title.x = element_text(color = "black", size = 10),
        axis.text.x = element_blank(),
        axis.ticks.x = element_blank(),
        axis.line.x = element_blank(),
        axis.title.y = element_text(color = "black", size = 10),
        axis.text.y = element_blank(),
        axis.ticks.y = element_blank(),
        axis.line.y = element_blank(),
        legend.position = "none",
        legend.title = element_text(size = 8),
        legend.text = element_text(size = 8),
        legend.key.size = unit(5, "pt"),
        panel.border = element_rect(color = "black", size = 1),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())
  
admixTheme = theme(
  panel.grid = element_blank(),
  panel.background = element_rect(fill = "gray85"),
  plot.background = element_blank(),
  panel.border = element_rect(fill = NA, color = "black", size = 0.75, linetype = "solid"),
  panel.spacing.x = grid:::unit(0.05, "lines"),
  panel.spacing.y = grid:::unit(0.05, "lines"),
  axis.text.x = element_blank(),
  axis.text.y = element_blank(),
  axis.ticks.x = element_blank(),
  axis.ticks.y = element_blank(),
  axis.title = element_blank(),
  strip.background.x = element_blank(),
  strip.background.y = element_blank(),
  strip.text = element_text(size = 8),
  strip.text.y.left = element_text(size = 10, angle = 90),
  strip.text.x.bottom = element_text(vjust = 1, color = NA),
  legend.key = element_blank(),
  legend.position = "none",
  legend.title = element_text(size = 8))

fstTheme = theme(
  axis.text.x = element_text(vjust = 3.5, size = 10, hjust = 0.5, color = "white"),
  axis.text.y = element_text(size = 10, color = "white", angle = 90, hjust = 0.5, vjust = -1.5),
  axis.title.x = element_blank(),
  axis.title.y = element_blank(),
  panel.grid.major = element_blank(),
  panel.border = element_blank(),
  axis.ticks = element_blank(),
  legend.title = element_text(size = 8, color = "black"),
  legend.text = element_text(size = 8, color = "black"),
  legend.position = c(0.6, 0.9),
  plot.background = element_blank(),
  panel.background = element_blank(),
)

violinTheme = theme(axis.title = element_text(color = "black", size = 12),
        axis.ticks.x = element_blank(),
        axis.text.x = element_text(color = "black", size = 10),
        legend.position = "none",
        legend.key.size = unit(0.3, 'cm'),
        panel.border = element_rect(color = "black", size = 1),
        panel.background = element_blank(),
        plot.background = element_blank(),
        panel.grid.major = element_blank(),
        panel.grid.minor = element_blank())

Sampling info

Map of study sites

flSites = read.csv("../data/flXestoMetaData.csv", header = TRUE)[-c(7, 15, 16, 32, 125, 126, 165, 197, 198, 253, 254, 314, 315, 353, 354),]
flSites$depthZone = factor(flSites$depthZone)
flSites$depthZone = factor(flSites$depthZone, levels = levels(flSites$depthZone)[c(2,1)])

flSites$region = factor(flSites$region)
flSites$region = factor(flSites$region, levels = levels(flSites$region)[c(3, 8, 1, 2, 7, 4, 6, 5)])
flSites$date = mdy(flSites$date) %>% format("%d %b %Y")

flPops = flSites %>% group_by(region) %>% summarise(latDD = mean(latDD), longDD = mean(longDD), n = n()) %>% droplevels()

flSampleSites = flSites %>% group_by(region, site, depthZone) %>% summarise(latDD = min(latDD), longDD = min(longDD))

## `summarise()` has grouped output by 'region', 'site'. You can override using the
## `.groups` argument.

fknmsBounds = read.csv("../data/shp/fknmsSPA.csv", header = TRUE)
coralECA = read_sf("../data/shp/SEFLCoralReefEcosystemConservationArea.shp") %>% st_transform(crs = 4326)
states = st_as_sf(ne_states(country = c("United States of America")), scale = "count",  crs = 4326) %>% filter(name_en %in% c("Florida", "Georgia", "Alabama"))
countries = st_as_sf(ne_countries(country = c("Cuba", "Mexico", "The Bahamas", "Bermuda"), scale = "Large"), crs = 4326)
bahamas = read_sf("../data/shp/bahamasShoreline.shp") %>% st_transform(crs = 4326)
cuba = read_sf("../data/shp/cubaShoreline.shp") %>% st_transform(crs = 4326)
florida = read_sf("../data/shp/floridaShoreline.shp") %>% st_transform(crs = 4326)
bathy = read_sf("../data/shp/flBathy.shp") %>% st_transform(crs = 4326) %>% subset(subset = DATASET %in% c("fl_shelf", "fl_coast"))
tortugasBathy = read_sf("../data/shp/tortugasBathy.shp") %>% st_transform(crs = 4326)

Next we build a hi-res polygon of FL with the study site marked and a zoomed in map of the colony locations. We use ggspatial to add a north arrow and scale bar to the main map.

floridaMap = ggplot() +
  geom_polygon(data = fknmsBounds[fknmsBounds$type == "Sanctuary",], aes(x = long, y = lat, group = location), alpha = 0.1, fill = "black", color =  "black") +
  geom_polygon(data = fknmsBounds[fknmsBounds$location == "FKNMS2",], aes(x = long, y = lat), fill = "aliceblue", color = NA) +
   geom_sf(data = coralECA, fill = "black", color = "black", alpha = 0.1, linewidth = 0.5) +
  # geom_polygon(data = fknmsBounds, aes(x = long, y = lat, color = type, group = location), fill = NA, linewidth = 0) +
  scale_fill_manual(values = flPal, name = "Site") +
  scale_color_manual(values = c("gray30",purple), name = "Boundaries", labels = c("FKNMS", "SPA")) +
  
  scale_shape_manual(values = c(21, 23), name = "Depth") +
  geom_sf(data = florida, fill = "white", linewidth = 0.15) +
  geom_sf(data = cuba, fill = "white", linewidth = 0.15) +
  geom_sf(data = bahamas, fill = "white", linewidth = 0.15) +
  geom_point(data = flSampleSites, aes(x = longDD, y = latDD, shape = depthZone, fill = region), color = "gray30", size = 3, alpha = 1) +
  coord_sf(xlim = c(-83.25, -80), ylim = c(24.25, 27.25)) +
  scale_x_continuous(breaks = c(seq(-83, -80, by = 1))) +
  scale_y_continuous(breaks = c(seq(23, 27, by = 1))) +
  annotation_scale(location = "br", pad_x = unit(1.35, "cm"), text_pad = unit(-4.5, "cm")) +
  guides(fill = guide_legend(override.aes = list(shape = 22, color = "gray30", size = 3), order = 1), shape = guide_legend(override.aes = list(size = c(2.25, 2), stroke = 0.25, color = "black"), order = 2), color = "none") +
  theme_bw() +
  theme(panel.background = element_rect(fill = "aliceblue"),

        plot.background = element_blank(),
        panel.border = element_rect(color = "black", size = 1, fill = NA),
        axis.title = element_blank(),
        axis.ticks = element_line(color = "black"),
        axis.text = element_text(color = "black"),
        legend.position = c(0.105, 0.35),
        legend.box.background = element_rect(linewidth = 0.35, fill = "white"),
        legend.title = element_text(color = "black", size = 8),
        legend.text = element_text(color = "black", size = 8),
        legend.spacing = unit(-5, "pt"),
        legend.key.size = unit(5, "pt"),
        legend.background = element_blank()
        )

# floridaMap

largeMap = inset = ggplot() +
  geom_sf(data = states, fill = "white", linewidth = 0.3) +
  geom_sf(data = countries, fill = "white", linewidth = 0.3) +
  geom_rect(aes(xmin = -83.25, xmax = -80, ymin = 24.25, ymax = 27.25), color = "black", fill = NA, alpha = 0.25, linewidth = 0.5) +
  geom_rect(aes(xmin = -78.8, xmax = -77, ymin = 22.2, ymax = 22.6), fill = "aliceblue", color = NA) +
  annotation_scale(location = "bl", pad_x = unit(2.25, "cm")) +
  annotation_north_arrow(location = "tr", style = north_arrow_minimal(), pad_x = unit(-0.3, "cm")) +
  coord_sf(xlim = c(-87, -76), ylim = c(22, 31)) +
  theme_bw() +
  theme(legend.title = element_text(size = 9, face = "bold"),
        axis.ticks = element_blank(),
        axis.text = element_blank(),
        axis.title = element_blank(),
        panel.background = element_rect(fill = "aliceblue"),
        panel.border = element_rect(color = "black", size = 1, fill = NA),
        legend.position = "none",
        plot.background = element_blank())

# largeMap

map = (floridaMap + 
  inset_element(largeMap, top = 1.07, right = 0.33, bottom = 0.63, left = -0.005, ignore_tag = TRUE))
  
ggsave("../figures/figure1.png", plot = map, height = 7, width = 7, units = "in", dpi = 300)

ggsave("../figures/figure1.svg", plot = map, height = 7, width = 7, units = "in", dpi = 300)

X. muta population genetics from SNPs

Analyzing 2bRAD generated SNPs (XXX loci) for population structure//genetic connectivity across sites and depth zones in FL

How many reads?

# xestoReads = read.delim("../data/snps/sintRawReadCounts", header = FALSE)
# colnames(xestoReads) = c("sample", "reads")
# 
# head(xestoReads)
# 
# #total reads
# sum(xestoReads$reads)
# 
# #average reads/sample
# (sum(xestoReads$reads)/366)

Identifiying clonal multi-locus genotypes

Dendrogram with clones

Identification of any natural clones using technical replicates as a baseline for clonality between samples.

cloneBams = read.csv("../data/flXestoMetaData.csv") %>% dplyr::select(-sampleID, -date, -species)# list of bam files

cloneMa = as.matrix(read.table("../data/clones/xestoClones3.ibsMat")) # reads in IBS matrix produced by ANGSD 

dimnames(cloneMa) = list(cloneBams[,1],cloneBams[,1])
clonesHc = hclust(as.dist(cloneMa), "ave")

cloneSites = cloneBams$region
cloneDepth = cloneBams$depthZone

cloneDend = cloneMa %>% as.dist() %>% hclust(., "ave") %>% as.dendrogram()
cloneDData = cloneDend %>% dendro_data()

# Making the branches hang shorter so we can easily see clonal groups
cloneDData$segments$yend2 = cloneDData$segments$yend
for(i in 1:nrow(cloneDData$segments)) {
  if (cloneDData$segments$yend2[i] == 0) {
    cloneDData$segments$yend2[i] = (cloneDData$segments$y[i] - 0.01)}}

cloneDendPoints = cloneDData$labels
cloneDendPoints$site = cloneSites[order.dendrogram(cloneDend)]
cloneDendPoints$depth=cloneDepth[order.dendrogram(cloneDend)]
rownames(cloneDendPoints) = cloneDendPoints$label

# Making points at the leaves to place symbols for populations
point = as.vector(NA)
for(i in 1:nrow(cloneDData$segments)) {
  if (cloneDData$segments$yend[i] == 0) {
    point[i] = cloneDData$segments$y[i] - 0.01
  } else {
    point[i] = NA}}

cloneDendPoints$y = point[!is.na(point)]

techReps = c("FKX014.1","FKX014.2", "FKX014.3", "FKX029.1", "FKX029.2", "FKX121.1", "FKX121.2", "FKX121.3", "FKX159.1", "FKX159.2", "FKX190.1", "FKX190.2", "FKX190.3", "SFX012.1", "SFX012.2", "SFX012.3", "SFX071.1", "SFX071.2", "SFX071.3", "SFX108.1", "SFX108.2", "SFX108.3")

cloneDendPoints$depth = factor(cloneDendPoints$depth)
cloneDendPoints$depth = factor(cloneDendPoints$depth,levels(cloneDendPoints$depth)[c(2,1)])

cloneDendPoints$site = factor(cloneDendPoints$site)
cloneDendPoints$site = factor(cloneDendPoints$site,levels(cloneDendPoints$site)[c(3, 8, 1, 2, 7, 4, 6, 5)])

cloneDendA = ggplot() +
  geom_segment(data = segment(cloneDData), aes(x = x, y = y, xend = xend, yend = yend2), size = 0.5) +
  geom_point(data = cloneDendPoints, aes(x = x, y = y, fill = site, shape = depth), size = 4, stroke = 0.25) +
  #scale_fill_brewer(palette = "Dark2", name = "Population") +
  scale_fill_manual(values = flPal, name= "Population")+
  scale_shape_manual(values = c(24, 25), name = "Depth Zone")+
  geom_hline(yintercept = 0.145, color = pink, lty = 5, size = 0.75) + # creating a dashed line to indicate a clonal distance threshold
  geom_text(data = subset(cloneDendPoints, subset = label %in% techReps), aes(x = x, y = (y - .015), label = label), angle = 90) + # spacing technical replicates further from leaf
  geom_text(data = subset(cloneDendPoints, subset = !label %in% techReps), aes(x = x, y = (y - .010), label = label), angle = 90) +
  labs(y = "Genetic distance (1 - IBS)") +
  guides(fill = guide_legend(override.aes = list(shape = 22)))+
  theme_classic()

cloneDend = cloneDendA + theme(
  axis.title.x = element_blank(),
  axis.text.x = element_blank(),
  axis.line.x = element_blank(),
  axis.ticks.x = element_blank(),
  axis.title.y = element_text(size = 12, color = "black", angle = 90),
  axis.text.y = element_text(size = 10, color = "black"),
  axis.line.y = element_line(),
  axis.ticks.y = element_line(),
  panel.grid = element_blank(),
  panel.border = element_blank(),
  panel.background = element_blank(),
  plot.background = element_blank(),
  legend.key = element_blank(),
  legend.title = element_text(size = 12),
  legend.text = element_text(size = 10),
  legend.position = "bottom")

cloneDend

ggsave("../figures/rmd/cloneDend.png", plot = cloneDend, height = 8, width = 40, units = "in", dpi = 300)

We removed the technical replicates/clones and re-ran ANGSD for all the following pop-gen analyses.

Dendrogram without clones

bams = read.csv("../data/flXestoMetaData.csv")[-c(7, 15, 16, 32, 125, 126, 165, 197, 198, 253, 254, 314, 315, 353, 354),] # list of bams files and their populations (tech reps removed)
bams$sample <- gsub("\\.[1-3]*$", "", bams$sample)

bams$region = factor(bams$region)
bams$region = factor(bams$region, levels = levels(bams$region)[c(3, 8, 1, 2, 7, 4, 6, 5)])

bams$depthZone = factor(bams$depthZone)
bams$depthZone = factor(bams$depthZone, levels = levels(bams$depthZone)[c(2,1)])

# ma = as.matrix(read.table("../data/ftl/xestoFTL.ibsMat"))
ma = as.matrix(read.table("../data/xestoNoClones.ibsMat")) # reads in IBS matrix produced by ANGSD


dimnames(ma) = list(bams[,3],bams[,3])


## admixture K = 2
#-------------------------------------
K2ad = read.table("../data/admix/noClones/K2.output") %>% dplyr::select(V6, V7) 
K2ad %>% summarise(sum(V6),sum(V7))

##    sum(V6) sum(V7)
## 1 301.7527 49.2473

admixK2 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K2ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7")
admixK2_melt = melt(admixK2, id = c("sample", "site", "depth", "depthm"))

## admixture K = 3
#-------------------------------------
K3ad = read.table("../data/admix/noClones/K3.output") %>% dplyr::select(V6, V7, V8) 
K3ad %>% summarise(sum(V6),sum(V7), sum(V8))

##    sum(V6) sum(V7) sum(V8)
## 1 211.2603 43.1265 96.6129

admixK3 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K3ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8") %>%
  dplyr::select(order(colnames(.)))
admixK3_melt = melt(admixK3, id = c("sample", "site", "depth", "depthm"))


## ngsAdmix K = 4
#-------------------------------------
K4ad = read.table("../data/admix/noClones/K4.output") %>% dplyr::select(V6, V7, V8, V9) 
K4ad %>% summarise(sum(V6),sum(V7), sum(V8), sum(V9))

##    sum(V6) sum(V7) sum(V8) sum(V9)
## 1 162.8505 38.5994 81.0511 68.4982

admixK4 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K4ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8", "Xm4" = "V9") %>%
  dplyr::select(order(colnames(.)))
admixK4_melt = melt(admixK4, id = c("sample", "site", "depth", "depthm"))


## admixture K = 5
#-------------------------------------
K5ad = read.table("../data/admix/noClones/K5.output") %>% dplyr::select(V6, V7, V8, V9, V10)
K5ad %>% summarise(sum(V6),sum(V7), sum(V8), sum(V9), sum(V10))

##    sum(V6) sum(V7) sum(V8) sum(V9) sum(V10)
## 1 103.7482 37.3177 71.0979 57.7997  81.0367

admixK5 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K5ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8", "Xm4" = "V9", "Xm5" = "V10") #%>%
admixK5_melt = melt(admixK5, id = c("sample", "site", "depth", "depthm"))

## construct figure
#-------------------------------------
# ggtree(tr) + geom_nodelab(aes(label = node), hjust = -0.5) 

{
  tr = hclust(dist(ma),"ave") 

  p1 = ggtree(tr, layout = "rectangular", size = 0.35) +  
    geom_point2(aes(subset = (node == 354)), shape = 21, size = 4.5, fill = xestoKColPal[2]) +
    geom_point2(aes(subset = (node == 357)), shape = 21, size = 4.5, fill=xestoKColPal[6]) +
    geom_point2(aes(subset = (node == 358)), shape = 21, size = 4.5, fill = xestoKColPal[1])

  p2 = facet_plot(p1, panel = "location", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = site), color = "grey25", size = 0.1) + 
    scale_fill_manual("Site", values = flPal) + 
    new_scale_fill() 

  p3 = facet_plot(p2, panel = "depth zone", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = depth), color = "grey25", size = 0.1) +
    scale_fill_manual("Depth zone", values = c("#A7E1BCFF", "#414083FF")) +
    new_scale_fill()
  
  p4 = facet_plot(p3, panel = "depth", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = depthm), color = "grey25", size = 0.1) + 
    scale_fill_viridis_c("Depth (m)", option = "mako", trans = "reverse") +
    new_scale_fill()

  p5 = facet_plot(p4, panel="K = 2", data=admixK2_melt, geom=geom_barh, width = 1.0, mapping = aes(x = value, fill = variable), 
                stat='identity', color = "grey25", size = 0.1) +
    scale_fill_manual("Lineage",values = xestoKColPal[1:5])

  p6 = facet_plot(p5, panel="K = 3", data=admixK3_melt, geom=geom_barh, width = 1.0, mapping = aes(x = value, fill = variable), 
                  stat='identity', color = "grey25", size = 0.1)  

  p7 = facet_plot(p6, panel="K = 4", data=admixK4_melt, geom=geom_barh, width = 1.0, mapping = aes(x = value, fill = variable), 
                  stat='identity', color = "grey25", size = 0.1)  

  p8 = facet_plot(p7, panel="K = 5", data=admixK5_melt, geom=geom_barh, width = 1.0, mapping = aes(x = value, fill = variable), 
                  stat='identity', color = "grey25", size = 0.1) +
    theme_tree(strip.text = element_blank(),
               panel.spacing = unit(.1, "line")) 
}

## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.

structure = facet_widths(p8, widths = c(0.8, 0.025, 0.025, 0.025, 0.25, 0.15, 0.15, 0.15))

# structure

Population structure

PCA

cov = read.table("../data/pcangsd/flXestoPcangsd.cov") %>% as.matrix()

# pcAdmix = read.table("../data/K3.output") %>% dplyr::select(V6, V7, V8)
# pcAdmix %>% summarise(sum(V6),sum(V7), sum(V8))


pcAdmix = read.table("../data/admix/noClones/K4.output") %>% dplyr::select(V6, V7, V8, V9)
pcAdmix %>% summarise(sum(V6),sum(V7), sum(V8), sum(V9))

##    sum(V6) sum(V7) sum(V8) sum(V9)
## 1 162.8505 38.5994 81.0511 68.4982

# pcAdmix = pcAdmix %>% dplyr::rename("cluster1" = "V6", "cluster2" = "V7", "cluster3" = "V8") %>% dplyr::select(order(colnames(.)))

pcAdmix = pcAdmix %>% dplyr::rename("cluster1" = "V6", "cluster2" = "V7", "cluster3" = "V8", "cluster4" = "V9") %>% dplyr::select(order(colnames(.)))
  
pcaEig = eigen(cov)
xestoPcaVar = pcaEig$values/sum(pcaEig$values)*100
head(xestoPcaVar)

## [1] 5.839551 2.713174 2.008476 1.797844 1.294318 1.241920

pcangsd = read.csv("../data/flXestoMetaData.csv")[-c(7, 15, 16, 32, 125, 126, 165, 197, 198, 253, 254, 314, 315, 353, 354),] %>%  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% cbind(pcAdmix)

pcangsd$sitedepth = as.factor(paste(pcangsd$site, pcangsd$depth, sep = " "))

pcangsd$sitedepth = factor(pcangsd$sitedepth)
pcangsd$sitedepth = factor(pcangsd$sitedepth, levels(pcangsd$sitedepth)[c(3, 12, 1, 2, 11, 10, 5, 4, 9, 8, 7, 6)])

pcangsd$site = factor(pcangsd$site)
pcangsd$site = factor(pcangsd$site, levels(pcangsd$site)[c(3, 8, 1, 2, 7, 4, 6, 5)])

pcangsd$depth = factor(pcangsd$depth)
pcangsd$depth = factor(pcangsd$depth, levels(pcangsd$depth)[c(2, 1)])

pcangsd$PC1 = pcaEig$vectors[,1]
pcangsd$PC2 = pcaEig$vectors[,2]
pcangsd$PC3 = pcaEig$vectors[,3]
pcangsd$PC4 = pcaEig$vectors[,4]

# pcangsdClust = pcAdmix %>% mutate(cluster = ifelse(cluster1 < 0.75 & cluster2 < 0.75  & cluster3 < 0.75, "NA", ifelse(cluster1 >=0.75, 1, ifelse(cluster2 >= 0.75, 2, ifelse(cluster3 >= 0.75, 3, 0)))))

pcangsdClustK2 = admixK2 %>% mutate(clusterK2 = ifelse(Xm1 >=0.75, "Xm1", ifelse(Xm2 >= 0.75, "Xm2", "Admixed")))
pcangsdClustK2$clusterK2 = as.factor(pcangsdClustK2$clusterK2)
levels(pcangsdClustK2$clusterK2)

## [1] "Admixed" "Xm1"     "Xm2"

pcangsdClustK2$clusterK2 = factor(pcangsdClustK2$clusterK2, levels = levels(pcangsdClustK2$clusterK2)[c(2,3,1)])


pcangsdClustK4 = admixK4 %>% mutate(clusterK4 = ifelse(Xm1 >=0.75, "Xm1", ifelse(Xm2 >= 0.75, "Xm2", ifelse(Xm3 >= 0.75, "Xm3", ifelse(Xm4 >= 0.75, "Xm4", "Admixed")))))
pcangsdClustK4$clusterK4 = as.factor(pcangsdClustK4$clusterK4)
levels(pcangsdClustK4$clusterK4)

## [1] "Admixed" "Xm1"     "Xm2"     "Xm3"     "Xm4"

pcangsdClustK4$clusterK4 = factor(pcangsdClustK4$clusterK4, levels = levels(pcangsdClustK4$clusterK4)[c(2,3,4,5,1)])


pcangsd = pcangsd %>% mutate(clusterK2 = pcangsdClustK2$clusterK2, clusterK4 = pcangsdClustK4$clusterK4)

# bamsClusters = pcangsd %>% dplyr::select(sample, cluster) %>% dplyr::arrange(sample) 
# bamsSamples = read.delim("../data/snps/bamsNoClones", header = FALSE)
# bamsClusters$sample = bamsSamples$V1

# bamsClusters = as.data.frame(bamsClusters)

# write.table(x = bamsClusters, file = "../data/snps/bamsClusters", sep = "\t", row.names = FALSE, col.names = FALSE, quote = FALSE)

pcangsd = merge(pcangsd, aggregate(cbind(mean.x = PC1, mean.y = PC2)~sitedepth, pcangsd, mean), by="sitedepth")

# set.seed(942)

# pcPerm = adonis2(pcangsd[6:9] ~ site*depth, data = pcangsd, permutations = 999, method = "euclidean")

# pcPerm

pcangsd %>% group_by(clusterK4) %>% dplyr::summarize(n = n(),  prop = n*0.75)

## # A tibble: 5 × 3
##   clusterK4     n  prop
##   <fct>     <int> <dbl>
## 1 Xm1          59  44.2
## 2 Xm2          19  14.2
## 3 Xm3          17  12.8
## 4 Xm4          12   9  
## 5 Admixed     244 183

pcangsd %>% group_by(depth,clusterK4) %>% dplyr::summarize(n = n())

## `summarise()` has grouped output by 'depth'. You can override using the `.groups`
## argument.

## # A tibble: 9 × 3
## # Groups:   depth [2]
##   depth      clusterK4     n
##   <fct>      <fct>     <int>
## 1 Shallow    Xm1          55
## 2 Shallow    Xm2          19
## 3 Shallow    Xm3          15
## 4 Shallow    Xm4           3
## 5 Shallow    Admixed     148
## 6 Mesophotic Xm1           4
## 7 Mesophotic Xm3           2
## 8 Mesophotic Xm4           9
## 9 Mesophotic Admixed      96

Plot PCA

pcaPlotSA = ggplot() +
  geom_hline(yintercept = 0, color = "gray90", size = 0.25) +
  geom_vline(xintercept = 0, color = "gray90", size = 0.25) +
  geom_point(data = pcangsd, aes(x = PC1, y = PC2, fill = site, shape = depth), color = "black", stroke = 0.25, size = 4, alpha = 0.5, show.legend = FALSE) +
  geom_point(data = pcangsd, aes(x = mean.x, y = mean.y, fill = site, shape = depth), color = "black", size = 5, alpha = 1, stroke = 0.5) +
  scale_shape_manual(values = c(21, 23), name = "Depth Zone") +
  scale_fill_manual(values = flPal, name = "Site") +
  scale_color_manual(values = flPal, name = "Site") +
  labs(x = paste0("PC 1 (", format(round(xestoPcaVar[1], 1), nsmall = 1)," %)"), y = paste0("PC 2 (", format(round(xestoPcaVar[2], 1), nsmall = 1), " %)")) +
  guides(shape = guide_legend(override.aes = list(size = 2, stroke = 0.25, alpha = NA), order = 2, ncol = 1), fill = guide_legend(override.aes = list(shape = 22, size = 2, fill = flPal, alpha = NA), order = 1, ncol = 1)) +
  theme_bw()

pcaPlotS = pcaPlotSA +
  pcaTheme +
  theme(legend.position = c(0.15, 0.25))


pcaPlotK4A = ggplot() +
  geom_hline(yintercept = 0, color = "gray90", size = 0.5) +
  geom_vline(xintercept = 0, color = "gray90", size = 0.5) +
  geom_point(data = pcangsd, aes(x = PC1, y = PC2, fill = clusterK4, shape = depth), color = "black", size = 4, alpha = 1, show.legend = TRUE) +
  scale_shape_manual(values = c(21, 23), name = "Depth Zone") +
  scale_fill_manual(values = xestoKColPal[c(1:4,6)], name = "Lineage") +
  labs(x = paste0("PC 1 (", format(round(xestoPcaVar[1], 1), nsmall = 1)," %)"), y = paste0("PC 2 (", format(round(xestoPcaVar[2], 1), nsmall = 1), " %)")) +
  guides(shape = "none", fill = guide_legend(override.aes = list(shape = 22, size = 2, fill = xestoKColPal[c(1:4,6)], alpha = NA), order = 1, ncol = 1))+
  theme_bw()

pcaPlotK4 = pcaPlotK4A +
  pcaTheme +
  theme(legend.position = c(0.12, 0.20))


pcaPlotK2A = ggplot() +
  geom_hline(yintercept = 0, color = "gray90", size = 0.25) +
  geom_vline(xintercept = 0, color = "gray90", size = 0.25) +
  geom_point(data = pcangsd, aes(x = PC1, y = PC2, fill = clusterK2, shape = depth), color = "black", size = 4, show.legend = FALSE) +
  scale_shape_manual(values = c(21, 23), name = "Depth Zone") +
  scale_fill_manual(values = c(xestoKColPal[c(1,2,6)]), name = "Site") +
  labs(x = paste0("PC 1 (", format(round(xestoPcaVar[1], 1), nsmall = 1)," %)"), y = paste0("PC 2 (", format(round(xestoPcaVar[2], 1), nsmall = 1), " %)")) +
  guides(shape = guide_legend(override.aes = list(size = 2, stroke = 0.25, alpha = NA), order = 2, ncol = 1), fill = guide_legend(override.aes = list(shape = 22, size = 2, fill = flPal, alpha = NA), order = 1, ncol = 1)) +
  theme_bw()

pcaPlotK2 = pcaPlotK2A +
  pcaTheme +
  theme(legend.position = c(0.15, 0.25))

Put all plots together

pcaPlots = (pcaPlotS | pcaPlotK4 | pcaPlotK2) +
  plot_annotation(tag_levels = 'A') &
  theme(plot.tag = element_text(size = 18),
        panel.background = element_rect(fill = "white"),
        legend.spacing = unit(-5, "pt"),
        legend.key = element_blank(),
        legend.background = element_blank())

pcaPlots

fig2 = (structure / pcaPlots) +
  plot_layout(heights = c(1.75, 1)) +
  plot_annotation(tag_levels = 'A') &
  theme(plot.tag = element_text(size = 20),
        legend.spacing = unit(-5, "pt"),
        legend.key = element_blank(),
        legend.background = element_blank())

ggsave("../figures/figure2.png", plot = fig2, height = 12, width = 14, units = "in", dpi = 300)
# ggsave("../figures/pcaPlots.svg", plot = pcaPlots, height = 4.5, width = 14, units = "in", dpi = 300)

Lineage demographics

K2ad = read.table("../data/admix/noClones/K2.output") %>% dplyr::select(V6, V7) 
K2ad %>% summarise(sum(V6),sum(V7))

##    sum(V6) sum(V7)
## 1 301.7527 49.2473

admixK2 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K2ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7")

k2lineage = admixK2 %>% mutate(cluster = ifelse(Xm1 >= .75, "Xm1", ifelse(Xm2 >= .75, "Xm2", "Admixed")))

K3ad = read.table("../data/admix/noCLones/K3.output") %>% dplyr::select(V6, V7, V8) 
K3ad %>% summarise(sum(V6),sum(V7), sum(V8))

##    sum(V6) sum(V7) sum(V8)
## 1 211.2603 43.1265 96.6129

admixK3 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K3ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8")

k3lineage = admixK3 %>% mutate(cluster = ifelse(Xm1 >= .75, "Xm1", ifelse(Xm2 >= .75, "Xm2", ifelse(Xm3 >= .75, "Xm3", "Admixed"))))

K4ad = read.table("../data/admix/noClones/K4.output") %>% dplyr::select(V6, V7, V8, V9) 
K4ad %>% summarise(sum(V6),sum(V7), sum(V8), sum(V9))

##    sum(V6) sum(V7) sum(V8) sum(V9)
## 1 162.8505 38.5994 81.0511 68.4982

admixK4 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K4ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8", "Xm4" = "V9")

k4lineage = admixK4 %>% mutate(cluster = ifelse(Xm1 >= .75, "Xm1", ifelse(Xm2 >= .75, "Xm2", ifelse(Xm3 >= .75, "Xm3", ifelse(Xm4 >= .75, "Xm4","Admixed")))))


k2Bams = k2lineage %>% select(sample, cluster)
k2Bams$sample = gsub("FK", "fk_", k2Bams$sample)
k2Bams$sample = gsub("SF", "sf_", k2Bams$sample)
k2Bams$sample = paste(k2Bams$sample, ".trim.bt2.bam", sep ="")

write_delim(k2Bams, "../data/k2bams", col_names = FALSE)

k3Bams = k3lineage %>% select(sample, cluster)
k3Bams$sample = gsub("FK", "fk_", k3Bams$sample)
k3Bams$sample = gsub("SF", "sf_", k3Bams$sample)
k3Bams$sample = paste(k3Bams$sample, ".trim.bt2.bam", sep ="")

write_delim(k3Bams, "../data/k3bams", col_names = FALSE)

k4Bams = k4lineage %>% select(sample, cluster)
k4Bams$sample = gsub("FK", "fk_", k4Bams$sample)
k4Bams$sample = gsub("SF", "sf_", k4Bams$sample)
k4Bams$sample = paste(k4Bams$sample, ".trim.bt2.bam", sep ="")

write_delim(k4Bams, "../data/k4bams", col_names = FALSE)

k2lineage %>% group_by(cluster) %>% summarise(n = n(), perc = n*0.75)

## # A tibble: 3 × 3
##   cluster     n  perc
##   <chr>   <int> <dbl>
## 1 Admixed    40  30  
## 2 Xm1       292 219  
## 3 Xm2        19  14.2

k3lineage %>% group_by(cluster) %>% summarise(n = n(), perc = n*0.75)

## # A tibble: 4 × 3
##   cluster     n  perc
##   <chr>   <int> <dbl>
## 1 Admixed   162 122. 
## 2 Xm1       138 104. 
## 3 Xm2        20  15  
## 4 Xm3        31  23.2

k4lineage %>% group_by(cluster) %>% summarise(n = n(), perc = n*0.75)

## # A tibble: 5 × 3
##   cluster     n  perc
##   <chr>   <int> <dbl>
## 1 Admixed   244 183  
## 2 Xm1        59  44.2
## 3 Xm2        19  14.2
## 4 Xm3        17  12.8
## 5 Xm4        12   9

hetK2Data = read.delim("../data/het/flXestoK2Het", header = FALSE, sep = " ") %>% rename("k2Het" = "V2") %>% mutate(sample = bams$sample) %>% left_join(pcangsdClustK2) %>% select(sample, k2Het, clusterK2)

## Joining with `by = join_by(sample)`

hetK4Data = read.delim("../data/het/flXestoK4Het", header = FALSE, sep = " ") %>% rename("k4Het" = "V2")%>% mutate(sample = bams$sample) %>% left_join(pcangsdClustK4) %>% select(sample, k4Het, clusterK4)

## Joining with `by = join_by(sample)`

xestoHet = bams %>% left_join(hetK2Data) %>% left_join(hetK4Data)

## Joining with `by = join_by(sample)`
## Joining with `by = join_by(sample)`

hetK2AOV = welch_anova_test(xestoHet, k2Het ~ clusterK2) 
hetK2PH = games_howell_test(xestoHet, k2Het ~ clusterK2)

hetK2PH$p.adj

## [1] 0.00000034800000 0.00000000000548 0.00003810000000

hetK2Letters = data.frame(x = factor(c("Xm1", "Xm2", "Admixed")), y = c(0.0025, 0.0025, 0.0025),  grp = c("a", "b", "c"))


hetK4AOV = welch_anova_test(xestoHet, k4Het ~ clusterK4) 
hetK4PH = games_howell_test(xestoHet, k4Het ~ clusterK4) 

hetK4PH$p.adj

##  [1] 0.00000084200 0.00006550000 0.07400000000 0.00000000782 0.00001210000 0.00000310000
##  [7] 0.00000596000 0.35100000000 0.41500000000 0.93400000000

hetK4Letters = data.frame(x = factor(c("Xm1", "Xm2", "Xm3", "Xm4","Admixed")), y = c(0.0025, 0.0025, 0.0025, 0.0025, 0.0025),  grp = c("a", "b", "c", "ac", "cd"))

hetPlotK2 = ggplot(data = xestoHet, aes(x = clusterK2, y = k2Het)) +
  geom_violin(aes(fill = clusterK2, group = clusterK2), adjust = 1, linewidth = 0.4, color = "black", alpha = 1, trim = TRUE, scale = "area", width = 1.2) +
  geom_boxplot(aes(fill = clusterK2, group = clusterK2), width = 0.2, color = "black", fill = "white", outlier.colour = NA, linewidth = 0.4, alpha = 0.5) +  xlab("Lineage") +
  geom_text(data = hetK2Letters, aes(x = x, y = y, label = grp), size = 4) +
   # annotate(geom = "text", x = 3.65, y =0.0036, label = bquote(italic("F")~" = "~.(hF)*"; "~italic("p")~" < 0.001"), size = 3) +
  scale_fill_discrete(type = xestoKColPal[c(1,2,6)], name = "Lineage") +
  xlab("Lineage") +
  ylab("Heterozygosity") +
  scale_y_continuous(breaks = seq(0, 0.0025, 0.0005)) +
  coord_cartesian(expand = TRUE, xlim = c(0.85, 3.15), ylim = c(0, 0.0025)) +
  theme_bw() + 
  violinTheme

hetPlotK2

hetPlotK4 = ggplot(data = xestoHet, aes(x = clusterK4, y = k4Het)) +
  geom_violin(aes(fill = clusterK4, group = clusterK4), adjust = 1, linewidth = 0.4, color = "black", alpha = 1, trim = TRUE, scale = "area", width = 1.2) +
  geom_boxplot(aes(fill = clusterK4, group = clusterK4), width = 0.2, color = "black", fill = "white", outlier.colour = NA, linewidth = 0.4, alpha = 0.5) +  xlab("Lineage") +
  geom_text(data = hetK4Letters, aes(x = x, y = y, label = grp), size = 4) +
   # annotate(geom = "text", x = 3.65, y =0.0036, label = bquote(italic("F")~" = "~.(hF)*"; "~italic("p")~" < 0.001"), size = 3) +
  scale_fill_discrete(type = xestoKColPal[c(1,2,3,4,6)], name = "Lineage") +
  xlab("Lineage") +
  ylab("Heterozygosity") +
  scale_y_continuous(breaks = seq(0, 0.0025, 0.0005)) +
  coord_cartesian(expand = TRUE, xlim = c(0.85, 5.15)) +
  theme_bw() +
  violinTheme

hetPlotK4

pop.order = c("Xm4", "Xm3", "Xm2", "Xm1")

# reads in fst 
fstMa1 <- read.delim("../data/xestoFstK4.out") %>% dplyr::select(-fst) %>% df_to_pw_mat(., "pop1", "pop2", "weightedFst")

fstMa1

##          Xm1      Xm2      Xm3      Xm4
## Xm1 0.000000 0.136042 0.033682 0.020161
## Xm2 0.136042 0.000000 0.113342 0.119521
## Xm3 0.033682 0.113342 0.000000 0.036817
## Xm4 0.020161 0.119521 0.036817 0.000000

fstMa = fstMa1

upperTriangle(fstMa, byrow = TRUE) <- lowerTriangle(fstMa)
fstMa <- fstMa[,pop.order] %>%
  .[pop.order,]
fstMa[upper.tri(fstMa)] <- NA
fstMa <- as.data.frame(fstMa)

# rearrange and reformat matrix
fstMa$Pop = factor(row.names(fstMa), levels = unique(pop.order))



# melt matrix data (turn from matrix into long dataframe)
fst = melt(fstMa, id.vars = "Pop", value.name = "Fst", variable.name = "Pop2", na.rm = FALSE)

fst$Fst = round(fst$Fst, 3)


fstHeatmap = ggplot(data = fst %>% filter(Fst != 0), aes(Pop, Pop2, fill = as.numeric(as.character(Fst)))) +
  geom_tile(color = "white") +
  geom_segment(data = fst, aes(x = 0.475, xend = 0.15, y = Pop2, yend = Pop2, color = Pop2), size = 20) + #colored boxes for Y-axis labels
  geom_segment(data = fst, aes(x = Pop, xend = Pop, y = 0.2, yend = 0.475, color = Pop), size = 22.5) + #colored boxes for X-axis labels
  scale_color_manual(values = rev(xestoKColPal[c(1:4)]), guide = NULL) +
  scale_fill_gradient(low = "white", high = "gray40", limit = c(0, 0.22), space = "Lab", name = expression(paste(italic("F")[ST])), na.value = NA,  guide = "colourbar") +
  geom_text(data = fst %>% filter(Fst != 0), aes(Pop, Pop2, label = Fst), color = "black", size = 3.5) +
  guides(fill = guide_colorbar(barwidth = 7.5, barheight = 0.75, title.position = "top", title.hjust = 0.5, direction = "horizontal", ticks.colour = "black", frame.colour = "black")) +
  scale_y_discrete(position = "left", limits = levels(fst$Pop2)) +
  scale_x_discrete(limits = rev(levels(fst$Pop2)[c(1:4)])) +
  coord_cartesian(xlim = c(1, 4), ylim = c(1, 4), clip = "off") +
  theme_minimal() +
  fstTheme

# fstHeatmap

Nucleotide diversity plot

npgList = list(read_tsv("../data/k2Xm1.thetas.idx.pestPG") %>% mutate(K = "*K*=2", lineage = "Xm1"),
               read_tsv("../data/k2Xm2.thetas.idx.pestPG") %>% mutate(K = "*K*=2", lineage = "Xm2"),
               read_tsv("../data/k4Xm1.thetas.idx.pestPG") %>% mutate(K = "*K*=4", lineage = "Xm1"),
               read_tsv("../data/k4Xm2.thetas.idx.pestPG") %>% mutate(K = "*K*=4", lineage = "Xm2"),
               read_tsv("../data/k4Xm3.thetas.idx.pestPG") %>% mutate(K = "*K*=4", lineage = "Xm3"),
               read_tsv("../data/k4Xm4.thetas.idx.pestPG") %>% mutate(K = "*K*=4", lineage = "Xm4"))

## Rows: 2377 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 2377 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 1855 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 1855 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 1855 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
## Rows: 1855 Columns: 14
## ── Column specification ────────────────────────────────────────────────────────────────
## Delimiter: "\t"
## chr  (2): #(indexStart,indexStop)(firstPos_withData,lastPos_withData)(WinStart,WinSt...
## dbl (12): WinCenter, tW, tP, tF, tH, tL, Tajima, fuf, fud, fayh, zeng, nSites
## 
## ℹ Use `spec()` to retrieve the full column specification for this data.
## ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

piAll = purrr::reduce(npgList, rbind) %>% 
  dplyr::group_by(K, lineage) %>%
  filter(tP != 0) %>%
  mutate(tPps = tP/nSites) %>%
  dplyr::summarize(tPps = mean(tPps))

## `summarise()` has grouped output by 'K'. You can override using the `.groups` argument.

piAll$Ne = (piAll$tPps)/(4*2e-8)
piAll

## # A tibble: 6 × 4
## # Groups:   K [2]
##   K     lineage    tPps     Ne
##   <chr> <chr>     <dbl>  <dbl>
## 1 *K*=2 Xm1     0.00407 50861.
## 2 *K*=2 Xm2     0.00540 67442.
## 3 *K*=4 Xm1     0.00438 54742.
## 4 *K*=4 Xm2     0.00659 82387.
## 5 *K*=4 Xm3     0.00467 58378.
## 6 *K*=4 Xm4     0.00434 54191.

piAll$K = factor(piAll$K)
piAll$lineage = factor(piAll$lineage)

nuclDivPlot = ggplot(piAll, aes(x = K, y = tPps, fill = lineage, group - lineage)) +
  geom_bar(position = position_dodge2(preserve = "single"), stat = "identity", color = "black") +
  scale_fill_manual(values = xestoKColPal) +
  geom_text(position = position_dodge2(preserve = "single", width = 0.9), aes(y = tPps-.0015, label= scales::comma(round(Ne,0)), hjust = 0, fontface = "bold"), angle = 90, color = "white", ) +
  labs(x = bquote(~italic(K)), y = bquote("Nucleotide diversity ("*pi*")")) + 
  coord_cartesian(xlim = c(0.4, 2.8), ylim = c(0, 0.007), expand = FALSE) +
  theme_bw() +
  violinTheme +
  theme(axis.text.x = ggtext::element_markdown())
  
nuclDivPlot

hetPlots = hetPlotK2 + hetPlotK4 + nuclDivPlot + fstHeatmap +
  plot_annotation(tag_levels = 'A') &
  theme(plot.tag = element_text(size = 14),
        legend.text = element_text(size = 8),
        legend.title = element_text(size = 10))
  
hetPlots

ggsave("../figures/figure4.png", plot = hetPlots, width = 8, height = 7, units = "in", dpi = 300)

Alternatively fixed snps

K3ad = read.table("../data/admix/noClones/K3.output") %>% dplyr::select(V6, V7, V8) 
K3ad %>% summarise(sum(V6),sum(V7), sum(V8))

##    sum(V6) sum(V7) sum(V8)
## 1 211.2603 43.1265 96.6129

admixK3 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K3ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7", "Xm3" = "V8")

admixK3afd = admixK3 %>% mutate(cluster = ifelse(Xm1 >= .97, "Xm1", ifelse(Xm2 >= .97, "Xm2", ifelse(between(Xm1, 0.40, 0.60) & between(Xm2, 0.40, 0.60) , "Hyb", ifelse(between(Xm1, 0.65, 0.85) & between(Xm2, 0.15, 0.35),"Hyb", ifelse(between(Xm2, 0.65, 0.85) & between(Xm1, 0.15, 0.35),"Hyb", "NA")))))) %>% filter(cluster != "NA")

admixK3afd %>% group_by(cluster) %>% summarise(n = n())

## # A tibble: 3 × 2
##   cluster     n
##   <chr>   <int>
## 1 Hyb        25
## 2 Xm1        59
## 3 Xm2        13

flXestoAdmixK3afd =  admixK3afd %>% filter(sample != "FKX006")
# 
# flXestoAdmixK3Melt = melt(flXestoAdmixK3afd, id.vars=c("sample", "site", "depth", "depthm"), variable.name="Ancestry", value.name="Fraction")

K2ad = read.table("../data/admix/noClones/K2.output") %>% dplyr::select(V6, V7) 
K2ad %>% summarise(sum(V6),sum(V7))

##    sum(V6) sum(V7)
## 1 301.7527 49.2473

admixK2 = bams %>%  
  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% 
  cbind(K2ad) %>% 
  dplyr::rename("Xm1" = "V6", "Xm2" = "V7")

admixK2afd = admixK2 %>% mutate(cluster = ifelse(Xm1 >= 1, "Xm1", ifelse(Xm2 >= 1, "Xm2", ifelse(between(Xm1, 0.40, 0.60) & between(Xm2, 0.40, 0.60) , "Hyb", ifelse(between(Xm1, 0.60, 0.90) & between(Xm2, 0.1, 0.40),"Hyb", ifelse(between(Xm2, 0.60, 0.90) & between(Xm1, 0.1, 0.40),"Hyb", "NA")))))) %>% filter(cluster != "NA")

flXestoAdmixK2 = admixK2afd %>% filter(sample %in% flXestoAdmixK3afd$sample) %>% arrange(-Xm1)
flXestoAdmixK2$ord = c(1:length(flXestoAdmixK2$sample)) 

flXestoAdmixK2Melt = melt(flXestoAdmixK2, id.vars=c("sample", "site", "depth", "depthm", "cluster", "ord"), variable.name="Lineage", value.name="Fraction")


admixPlotK2AFDa = ggplot(data = flXestoAdmixK2Melt, aes(x = ord, y = Fraction, fill = Lineage, order = ord)) +
  geom_bar(stat = "identity", position = "fill", width = 1, colour = "grey25", linewidth = 0.2) +
  scale_fill_manual(values = xestoKColPal) +
  scale_color_manual(values = rev(flPal)) +
  scale_x_discrete(expand = c(0, 0)) +
  scale_y_continuous(expand = c(0.001, 0.001)) +
  coord_cartesian(ylim = c(0.0, 1.0), clip = "off") +
theme_bw()


admixPlotK2AFD = admixPlotK2AFDa + 
  admixTheme +
  theme(legend.position = "right")

admixPlotK2AFD

afd_groups = data.frame("sample" = flXestoAdmixK2$sample, "group" = flXestoAdmixK2$cluster) %>% arrange(sample)

afd_groups$sample = gsub(pattern = "SF", replacement = "sf_", afd_groups$sample)
afd_groups$sample = gsub(pattern = "FK", replacement = "fk_", afd_groups$sample)
afd_groups$sample = paste(afd_groups$sample, ".trim.bt2.bam", sep = "")

afd_groups$sample

##  [1] "fk_X004.trim.bt2.bam" "fk_X016.trim.bt2.bam" "fk_X043.trim.bt2.bam"
##  [4] "fk_X051.trim.bt2.bam" "fk_X056.trim.bt2.bam" "fk_X059.trim.bt2.bam"
##  [7] "fk_X064.trim.bt2.bam" "fk_X068.trim.bt2.bam" "fk_X087.trim.bt2.bam"
## [10] "fk_X089.trim.bt2.bam" "fk_X100.trim.bt2.bam" "fk_X114.trim.bt2.bam"
## [13] "fk_X119.trim.bt2.bam" "fk_X122.trim.bt2.bam" "fk_X147.trim.bt2.bam"
## [16] "fk_X184.trim.bt2.bam" "fk_X186.trim.bt2.bam" "fk_X188.trim.bt2.bam"
## [19] "fk_X189.trim.bt2.bam" "fk_X205.trim.bt2.bam" "fk_X211.trim.bt2.bam"
## [22] "fk_X215.trim.bt2.bam" "fk_X219.trim.bt2.bam" "fk_X224.trim.bt2.bam"
## [25] "fk_X227.trim.bt2.bam" "fk_X229.trim.bt2.bam" "fk_X230.trim.bt2.bam"
## [28] "sf_X008.trim.bt2.bam" "sf_X012.trim.bt2.bam" "sf_X015.trim.bt2.bam"
## [31] "sf_X023.trim.bt2.bam" "sf_X024.trim.bt2.bam" "sf_X025.trim.bt2.bam"
## [34] "sf_X026.trim.bt2.bam" "sf_X028.trim.bt2.bam" "sf_X033.trim.bt2.bam"
## [37] "sf_X034.trim.bt2.bam" "sf_X036.trim.bt2.bam" "sf_X037.trim.bt2.bam"
## [40] "sf_X039.trim.bt2.bam" "sf_X040.trim.bt2.bam" "sf_X043.trim.bt2.bam"
## [43] "sf_X061.trim.bt2.bam" "sf_X063.trim.bt2.bam" "sf_X064.trim.bt2.bam"
## [46] "sf_X065.trim.bt2.bam" "sf_X066.trim.bt2.bam" "sf_X067.trim.bt2.bam"
## [49] "sf_X068.trim.bt2.bam" "sf_X071.trim.bt2.bam" "sf_X072.trim.bt2.bam"
## [52] "sf_X073.trim.bt2.bam" "sf_X076.trim.bt2.bam" "sf_X077.trim.bt2.bam"
## [55] "sf_X079.trim.bt2.bam" "sf_X080.trim.bt2.bam" "sf_X083.trim.bt2.bam"
## [58] "sf_X084.trim.bt2.bam" "sf_X086.trim.bt2.bam" "sf_X090.trim.bt2.bam"
## [61] "sf_X093.trim.bt2.bam" "sf_X094.trim.bt2.bam" "sf_X103.trim.bt2.bam"
## [64] "sf_X105.trim.bt2.bam" "sf_X107.trim.bt2.bam" "sf_X110.trim.bt2.bam"
## [67] "sf_X112.trim.bt2.bam" "sf_X113.trim.bt2.bam" "sf_X114.trim.bt2.bam"
## [70] "sf_X117.trim.bt2.bam" "sf_X119.trim.bt2.bam"

write_delim(afd_groups, "../data/afd_groups", col_names = FALSE)

afd_groups %>% select("sample") %>% write_delim(., "../data/afd_samples", col_names = FALSE)

maAFD = as.matrix(read.table("../data/xestoAFD.ibsMat"))

afdSamples = admixK2afd %>% filter(sample %in% flXestoAdmixK3afd$sample) %>% select(sample)

dimnames(maAFD) = list(afdSamples[,1],afdSamples[,1])


trafd = hclust(dist(maAFD),"ave") 

  p1afd = ggtree(trafd, layout = "rectangular") #+ ggtree::geom_tiplab()

  p2afd = facet_plot(p1afd, panel = "location", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = site), size = 0.1, color = "grey25") + 
    scale_fill_manual("Site", values = flPal, guide = guide_legend(ncol = 2, order = 1)) + 
    theme(legend.key.size = unit(.8, "line")) +
    new_scale_fill()

## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.

  p3afd = facet_plot(p2afd, panel = "depth zone", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = depth), size = 0.1, color = "grey25") +
    scale_fill_manual("Depth zone", values = c("#A7E1BCFF", "#414083FF"), guide = guide_legend(ncol = 2, order = 2)) +
    new_scale_fill()

## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.

  p4afd = facet_plot(p3afd, panel = "depth", data=admixK2, geom = geom_tile, mapping = aes(x = 1, fill = depthm), size = 0.1, color = "grey25") + 
    scale_fill_viridis_c("Depth (m)", option = "mako", direction = -1, guide = guide_colorbar(order = 2, direction = "horizontal")) +
    theme(legend.title.position = "top") +
    new_scale_fill()

## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.

  p5afd = facet_plot(p4afd, panel="K = 2", data = admixK2_melt, geom=geom_barh, width = 1.0, mapping = aes(x = value, fill = variable), 
                stat ='identity', size = 0.15, color = "grey25") +
    scale_fill_manual("Lineage",values = xestoKColPal[1:2], guide = guide_legend(ncol = 2, order = 4)) + 
    theme(strip.text = element_blank(),
          #legend.direction = "horizontal",
          legend.text = element_text(size = 8),
          legend.title = element_text(size = 10),
          legend.key = element_blank(),
          legend.margin = margin(c(0,0,0,0),unit = "pt"))

## ℹ invalid tbl_tree object. Missing column: parent,node.
## ℹ invalid tbl_tree object. Missing column: parent,node.

p5afd

afdTree =  facet_widths(p5afd, widths = c(0.25, 0.025, 0.025, 0.025, 0.25))

covAFD = read.table("../data/pcangsd/flXestoAFDPcangsd.cov") %>% as.matrix()

pcaEigAFD = eigen(covAFD)
xestoPcaVarAFD = pcaEigAFD$values/sum(pcaEigAFD$values)*100

head(xestoPcaVarAFD)

## [1] 17.668624  4.996007  1.747479  1.600818  1.570501  1.524815

pcangsdAFD = bams %>%  dplyr::select(sample, "site" = region, "depth" = depthZone, "depthm" = depthM) %>% filter(sample %in% flXestoAdmixK2$sample) %>% left_join(flXestoAdmixK2)

## Joining with `by = join_by(sample, site, depth, depthm)`

pcangsdAFD$PC1 = pcaEigAFD$vectors[,1]
pcangsdAFD$PC2 = pcaEigAFD$vectors[,2]
pcangsdAFD$PC3 = pcaEigAFD$vectors[,3]
pcangsdAFD$PC4 = pcaEigAFD$vectors[,4]

pcangsdAFD = pcangsdAFD %>% mutate(cluster = ifelse(Xm1 >= 0.98, "Xm1", ifelse(Xm2 >= 0.98, "Xm2", "Admixed")))


pcangsdAFD$cluster = as.factor(pcangsdAFD$cluster)
levels(pcangsdAFD$cluster)

## [1] "Admixed" "Xm1"     "Xm2"

pcangsdAFD$cluster = factor(pcangsdAFD$cluster, levels = levels(pcangsdAFD$cluster)[c(2, 3, 1)])